Query 036178
Match_columns 330
No_of_seqs 155 out of 222
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 10:12:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036178.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036178hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 1.4E-37 3E-42 237.0 3.9 61 29-89 2-62 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.6 0.027 5.9E-07 48.5 0.8 34 32-67 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 93.2 0.08 1.7E-06 37.2 2.5 29 31-65 17-45 (46)
4 COG3677 Transposase and inacti 92.6 0.086 1.9E-06 44.6 2.4 36 32-69 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 90.8 0.16 3.5E-06 35.3 1.8 31 32-64 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 88.6 0.49 1.1E-05 33.0 2.8 37 33-69 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.3 0.77 1.7E-05 31.8 2.3 36 33-68 1-39 (39)
8 PF13453 zf-TFIIB: Transcripti 81.0 0.51 1.1E-05 32.4 0.1 37 34-75 1-37 (41)
9 PF04216 FdhE: Protein involve 80.3 0.83 1.8E-05 42.0 1.2 38 31-68 210-249 (290)
10 TIGR01384 TFS_arch transcripti 76.6 2.6 5.6E-05 33.2 2.9 39 32-70 62-103 (104)
11 cd00202 ZnF_GATA Zinc finger D 76.1 2.2 4.7E-05 31.5 2.1 40 34-76 1-40 (54)
12 PHA02998 RNA polymerase subuni 75.8 2.8 6E-05 39.0 3.2 39 31-69 142-183 (195)
13 PF04981 NMD3: NMD3 family ; 74.0 1.8 3.8E-05 39.1 1.4 26 46-71 19-49 (236)
14 PF14690 zf-ISL3: zinc-finger 70.6 2.2 4.7E-05 29.1 1.0 32 32-63 2-47 (47)
15 PRK14810 formamidopyrimidine-D 67.4 3.9 8.4E-05 37.9 2.2 32 29-65 241-272 (272)
16 TIGR01385 TFSII transcription 67.0 4.8 0.0001 38.6 2.8 38 31-68 257-297 (299)
17 KOG2846 Predicted membrane pro 66.7 10 0.00023 37.5 5.1 36 27-65 215-250 (328)
18 PRK14811 formamidopyrimidine-D 63.5 5.2 0.00011 37.1 2.3 31 30-65 233-263 (269)
19 smart00401 ZnF_GATA zinc finge 62.6 6.3 0.00014 28.7 2.1 40 31-73 2-41 (52)
20 PRK01103 formamidopyrimidine/5 60.8 6.2 0.00013 36.4 2.2 31 30-65 243-273 (274)
21 TIGR00244 transcriptional regu 60.4 6.8 0.00015 34.9 2.3 44 34-77 2-48 (147)
22 PRK10445 endonuclease VIII; Pr 59.3 6.8 0.00015 36.1 2.2 30 31-65 234-263 (263)
23 PRK13945 formamidopyrimidine-D 57.5 7.9 0.00017 36.0 2.3 30 31-65 253-282 (282)
24 PF06220 zf-U1: U1 zinc finger 57.2 4.4 9.6E-05 28.2 0.5 17 55-71 1-17 (38)
25 PRK00464 nrdR transcriptional 55.7 8.7 0.00019 33.8 2.2 45 33-77 1-48 (154)
26 PHA00626 hypothetical protein 53.4 9.8 0.00021 29.8 1.9 36 34-71 2-37 (59)
27 PRK03564 formate dehydrogenase 52.7 9.6 0.00021 37.0 2.1 38 31-69 225-264 (309)
28 TIGR01562 FdhE formate dehydro 49.2 11 0.00024 36.4 2.0 38 31-69 223-264 (305)
29 PRK00432 30S ribosomal protein 48.3 10 0.00022 27.9 1.2 26 32-65 20-45 (50)
30 PF09526 DUF2387: Probable met 46.5 14 0.00031 29.0 1.9 31 32-65 8-38 (71)
31 COG0266 Nei Formamidopyrimidin 40.1 20 0.00043 34.5 2.1 31 30-65 243-273 (273)
32 PF14599 zinc_ribbon_6: Zinc-r 37.9 13 0.00029 28.6 0.5 14 31-44 47-60 (61)
33 KOG2906 RNA polymerase III sub 36.8 27 0.00059 30.0 2.2 39 30-68 63-104 (105)
34 COG4260 Membrane protease subu 36.7 17 0.00037 36.2 1.2 36 27-64 301-341 (345)
35 PF14354 Lar_restr_allev: Rest 34.7 35 0.00075 24.4 2.2 35 31-65 2-37 (61)
36 PF07282 OrfB_Zn_ribbon: Putat 34.4 23 0.00051 25.8 1.3 32 31-69 27-58 (69)
37 TIGR03655 anti_R_Lar restricti 32.4 39 0.00085 24.3 2.2 32 33-65 2-34 (53)
38 PF06827 zf-FPG_IleRS: Zinc fi 30.9 23 0.00049 22.8 0.7 27 33-64 2-28 (30)
39 COG1997 RPL43A Ribosomal prote 30.2 32 0.0007 28.8 1.6 44 29-79 32-75 (89)
40 COG1327 Predicted transcriptio 29.1 36 0.00077 31.0 1.8 44 34-77 2-48 (156)
41 PRK12496 hypothetical protein; 27.5 36 0.00078 29.8 1.5 12 58-69 128-139 (164)
42 PF08273 Prim_Zn_Ribbon: Zinc- 27.4 34 0.00074 24.4 1.1 32 32-65 3-34 (40)
43 PF01807 zf-CHC2: CHC2 zinc fi 26.9 40 0.00086 26.8 1.5 30 32-65 33-62 (97)
44 TIGR02443 conserved hypothetic 26.9 47 0.001 26.0 1.9 30 32-64 9-38 (59)
45 TIGR00686 phnA alkylphosphonat 25.6 50 0.0011 28.5 2.0 31 33-71 3-33 (109)
46 PF08274 PhnA_Zn_Ribbon: PhnA 25.3 34 0.00073 23.3 0.8 28 33-68 3-30 (30)
47 TIGR00595 priA primosomal prot 24.8 56 0.0012 32.9 2.5 34 30-64 220-260 (505)
48 PF06044 DRP: Dam-replacing fa 23.4 31 0.00066 33.4 0.4 33 32-68 31-64 (254)
49 PRK10220 hypothetical protein; 23.2 61 0.0013 28.1 2.1 32 32-71 3-34 (111)
50 PF01873 eIF-5_eIF-2B: Domain 22.4 69 0.0015 27.3 2.2 29 32-64 93-121 (125)
51 PRK14892 putative transcriptio 22.1 1E+02 0.0023 25.7 3.2 36 29-68 18-53 (99)
52 smart00661 RPOL9 RNA polymeras 21.4 63 0.0014 22.2 1.5 32 34-70 2-33 (52)
53 PTZ00255 60S ribosomal protein 20.8 63 0.0014 26.9 1.6 44 29-79 33-76 (90)
54 COG4049 Uncharacterized protei 20.7 37 0.00081 27.0 0.3 11 30-40 15-25 (65)
55 KOG2463 Predicted RNA-binding 20.4 31 0.00068 34.9 -0.2 38 31-83 241-278 (376)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=1.4e-37 Score=236.95 Aligned_cols=61 Identities=84% Similarity=1.578 Sum_probs=58.9
Q ss_pred CCCccCCCCCCCCCceeeeecccCCCCCCccccccccccccCcccccccCCCCcCCCCCCC
Q 036178 29 NHQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKTKRSS 89 (330)
Q Consensus 29 ~~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtLRNVPVGGG~RKnKrss 89 (330)
+++.++||||+|.||||||||||++.||||||++|+||||+||+||||||||||||+|+++
T Consensus 2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~ 62 (63)
T PF02701_consen 2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSS 62 (63)
T ss_pred CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCC
Confidence 4689999999999999999999999999999999999999999999999999999999876
No 2
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=93.58 E-value=0.027 Score=48.52 Aligned_cols=34 Identities=24% Similarity=0.705 Sum_probs=27.2
Q ss_pred ccCCCCCCCCCceeeeeccc--CCCCCCcccccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNY--NLSQPRHFCKNCRRYW 67 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNY--n~~QPRhfCKsCrRYW 67 (330)
...||||.|.+|+.. +.| +.++.-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 589999999999965 555 4567779999998643
No 3
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=93.19 E-value=0.08 Score=37.18 Aligned_cols=29 Identities=34% Similarity=0.787 Sum_probs=23.4
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
.+..||+|.+. ++..+.+ ..+|.|++|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 34779999998 6666666 78999999985
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.60 E-value=0.086 Score=44.59 Aligned_cols=36 Identities=31% Similarity=0.615 Sum_probs=28.5
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCcccccccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTK 69 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~ 69 (330)
...||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred cCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 47899999999 3335555555999999999998874
No 5
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=90.82 E-value=0.16 Score=35.30 Aligned_cols=31 Identities=39% Similarity=0.764 Sum_probs=21.7
Q ss_pred ccCCCCCCCCCceeeeecccCCC-CCCccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLS-QPRHFCKNCR 64 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~-QPRhfCKsCr 64 (330)
.+.||+|.+.+. -|=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence 478999999872 123444433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.57 E-value=0.49 Score=32.98 Aligned_cols=37 Identities=22% Similarity=0.693 Sum_probs=27.6
Q ss_pred cCCCCCCCCCceeeeecccCCCCC---Ccccccccccccc
Q 036178 33 LKCPRCDSLNTKFCYYNNYNLSQP---RHFCKNCRRYWTK 69 (330)
Q Consensus 33 l~CPRC~S~nTKFCYYNNYn~~QP---RhfCKsCrRYWT~ 69 (330)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 379999877777655555555555 4999999999963
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=85.30 E-value=0.77 Score=31.79 Aligned_cols=36 Identities=28% Similarity=0.747 Sum_probs=23.8
Q ss_pred cCCCCCCCCCceeeeecccCCCCCC---ccccccccccc
Q 036178 33 LKCPRCDSLNTKFCYYNNYNLSQPR---HFCKNCRRYWT 68 (330)
Q Consensus 33 l~CPRC~S~nTKFCYYNNYn~~QPR---hfCKsCrRYWT 68 (330)
.+||.|...+.-|=-.+.....-|- |.|.+|..-|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 3799999977665555555555443 89999999885
No 8
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=80.97 E-value=0.51 Score=32.42 Aligned_cols=37 Identities=27% Similarity=0.606 Sum_probs=27.2
Q ss_pred CCCCCCCCCceeeeecccCCCCCCccccccccccccCccccc
Q 036178 34 KCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRN 75 (330)
Q Consensus 34 ~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtLRN 75 (330)
+||+|...-...-+ ..-+-+.|..|.-.|=..|.+..
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence 69999985555444 23566889999999988776654
No 9
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=80.31 E-value=0.83 Score=42.04 Aligned_cols=38 Identities=24% Similarity=0.620 Sum_probs=19.1
Q ss_pred CccCCCCCCCCC-ceeeeecc-cCCCCCCccccccccccc
Q 036178 31 QALKCPRCDSLN-TKFCYYNN-YNLSQPRHFCKNCRRYWT 68 (330)
Q Consensus 31 ~~l~CPRC~S~n-TKFCYYNN-Yn~~QPRhfCKsCrRYWT 68 (330)
....||.|...+ .++-||.. -....--+.|+.|+.|+-
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 457899999855 56667633 333333499999999983
No 10
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=76.65 E-value=2.6 Score=33.17 Aligned_cols=39 Identities=18% Similarity=0.611 Sum_probs=28.0
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCC---ccccccccccccC
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPR---HFCKNCRRYWTKG 70 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPR---hfCKsCrRYWT~G 70 (330)
..+||+|...+.-|=..+-.+...|- |.|..|.-.|+.+
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 47999998776665554444433333 9999999999875
No 11
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=76.06 E-value=2.2 Score=31.55 Aligned_cols=40 Identities=30% Similarity=0.710 Sum_probs=28.1
Q ss_pred CCCCCCCCCceeeeecccCCCCCCccccccccccccCcccccc
Q 036178 34 KCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNV 76 (330)
Q Consensus 34 ~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtLRNV 76 (330)
.|--|...+|..=.-. ...+..+|-+|.-||.+.|..|.+
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCc
Confidence 3777877777532222 246779999999999999965544
No 12
>PHA02998 RNA polymerase subunit; Provisional
Probab=75.78 E-value=2.8 Score=38.97 Aligned_cols=39 Identities=26% Similarity=0.625 Sum_probs=33.6
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCC---cccccccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPR---HFCKNCRRYWTK 69 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPR---hfCKsCrRYWT~ 69 (330)
...+||+|...++-|--.|-.+-..|- |.|..|..-|.-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 568999999999998888888887775 899999999863
No 13
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=73.98 E-value=1.8 Score=39.08 Aligned_cols=26 Identities=27% Similarity=0.841 Sum_probs=18.4
Q ss_pred eeecccCCCC-----CCccccccccccccCc
Q 036178 46 CYYNNYNLSQ-----PRHFCKNCRRYWTKGG 71 (330)
Q Consensus 46 CYYNNYn~~Q-----PRhfCKsCrRYWT~GG 71 (330)
||...+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 5666665533 2379999999999843
No 14
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=70.62 E-value=2.2 Score=29.06 Aligned_cols=32 Identities=31% Similarity=0.684 Sum_probs=19.3
Q ss_pred ccCCCCCCCCCcee-eeecc---------c----CCCCCCcccccc
Q 036178 32 ALKCPRCDSLNTKF-CYYNN---------Y----NLSQPRHFCKNC 63 (330)
Q Consensus 32 ~l~CPRC~S~nTKF-CYYNN---------Y----n~~QPRhfCKsC 63 (330)
+..||.|.+..-+. -++.. + .+..+|++|++|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 46899999876221 11111 0 346778888887
No 15
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=67.40 E-value=3.9 Score=37.90 Aligned_cols=32 Identities=16% Similarity=0.590 Sum_probs=23.2
Q ss_pred CCCccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 29 NHQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 29 ~~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
..+..+||||...=.|.-+= .+.-|||..|++
T Consensus 241 ~R~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 241 QRTGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 34578999999866654442 366699999985
No 16
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=66.99 E-value=4.8 Score=38.60 Aligned_cols=38 Identities=16% Similarity=0.594 Sum_probs=28.2
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCC---ccccccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPR---HFCKNCRRYWT 68 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPR---hfCKsCrRYWT 68 (330)
...+||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 468999999777776555555555553 78999999884
No 17
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=66.72 E-value=10 Score=37.51 Aligned_cols=36 Identities=25% Similarity=0.456 Sum_probs=23.8
Q ss_pred CCCCCccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 27 HQNHQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 27 ~~~~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
+.+...+.|+.|..-|-=.-+ -.| .-.++.|..|..
T Consensus 215 P~~ryALIC~~C~~HNGla~~-ee~--~yi~F~C~~Cn~ 250 (328)
T KOG2846|consen 215 PNNRYALICSQCHHHNGLARK-EEY--EYITFRCPHCNA 250 (328)
T ss_pred CcchhhhcchhhccccCcCCh-hhc--CceEEECccccc
Confidence 345678999999887653322 222 235789999964
No 18
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=63.50 E-value=5.2 Score=37.08 Aligned_cols=31 Identities=29% Similarity=0.780 Sum_probs=22.8
Q ss_pred CCccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 30 HQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 30 ~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
.+..+||||...=.|.-+ . .+.-|||..|++
T Consensus 233 R~g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 233 REGQPCPRCGTPIEKIVV-G----GRGTHFCPQCQP 263 (269)
T ss_pred CCcCCCCcCCCeeEEEEE-C----CCCcEECCCCcC
Confidence 346789999987666433 2 366799999996
No 19
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=62.64 E-value=6.3 Score=28.74 Aligned_cols=40 Identities=25% Similarity=0.559 Sum_probs=29.4
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCCccccccccccccCccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVL 73 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtL 73 (330)
....|--|....|..=.- ...-++.+|-+|.-||.+.|.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~---g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRR---GPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCcccc---CCCCCCcEeecccHHHHHcCCC
Confidence 357899999888863322 2223379999999999998886
No 20
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=60.84 E-value=6.2 Score=36.36 Aligned_cols=31 Identities=23% Similarity=0.638 Sum_probs=22.5
Q ss_pred CCccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 30 HQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 30 ~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
....+||||...=.|. -++ .+.-|||..|++
T Consensus 243 R~g~pC~~Cg~~I~~~-~~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 243 REGEPCRRCGTPIEKI-KQG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCCeeEEE-EEC----CCCcEECcCCCC
Confidence 3567899999776553 333 366799999986
No 21
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=60.41 E-value=6.8 Score=34.91 Aligned_cols=44 Identities=23% Similarity=0.398 Sum_probs=32.6
Q ss_pred CCCCCCCCCceeeee---cccCCCCCCccccccccccccCccccccc
Q 036178 34 KCPRCDSLNTKFCYY---NNYNLSQPRHFCKNCRRYWTKGGVLRNVP 77 (330)
Q Consensus 34 ~CPRC~S~nTKFCYY---NNYn~~QPRhfCKsCrRYWT~GGtLRNVP 77 (330)
+||.|...+||+-== ..-+.-+-|.-|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998643 34445667899999999998655444433
No 22
>PRK10445 endonuclease VIII; Provisional
Probab=59.26 E-value=6.8 Score=36.13 Aligned_cols=30 Identities=27% Similarity=0.708 Sum_probs=22.0
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
...+||||...=.|.-+ . .+.-|||..|++
T Consensus 234 ~g~~Cp~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 263 (263)
T PRK10445 234 DGEACERCGGIIEKTTL-S----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCEeEEEEE-C----CCCcEECCCCcC
Confidence 46789999887665544 2 366799999984
No 23
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.55 E-value=7.9 Score=36.00 Aligned_cols=30 Identities=20% Similarity=0.665 Sum_probs=22.1
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
...+||||...=.|.-+= .+.-|||..|++
T Consensus 253 ~g~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 282 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLA-----GRSTHWCPNCQK 282 (282)
T ss_pred CcCCCCcCCCeeEEEEEC-----CCccEECCCCcC
Confidence 356999999876665442 266699999985
No 24
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=57.22 E-value=4.4 Score=28.22 Aligned_cols=17 Identities=35% Similarity=1.026 Sum_probs=7.1
Q ss_pred CCCccccccccccccCc
Q 036178 55 QPRHFCKNCRRYWTKGG 71 (330)
Q Consensus 55 QPRhfCKsCrRYWT~GG 71 (330)
+|||||.=|..|.+..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 25
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=55.73 E-value=8.7 Score=33.85 Aligned_cols=45 Identities=24% Similarity=0.463 Sum_probs=33.1
Q ss_pred cCCCCCCCCCceee---eecccCCCCCCccccccccccccCccccccc
Q 036178 33 LKCPRCDSLNTKFC---YYNNYNLSQPRHFCKNCRRYWTKGGVLRNVP 77 (330)
Q Consensus 33 l~CPRC~S~nTKFC---YYNNYn~~QPRhfCKsCrRYWT~GGtLRNVP 77 (330)
.+||-|.+..|++- |+-.-++-.-|+-|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999987764 4555555666799999999888766655554
No 26
>PHA00626 hypothetical protein
Probab=53.38 E-value=9.8 Score=29.84 Aligned_cols=36 Identities=22% Similarity=0.276 Sum_probs=24.4
Q ss_pred CCCCCCCCCceeeeecccCCCCCCccccccccccccCc
Q 036178 34 KCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGG 71 (330)
Q Consensus 34 ~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GG 71 (330)
.||+|.|.+--=|-.= ....-||.|++|.=++|+..
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 6999999754322111 11245799999999999864
No 27
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=52.68 E-value=9.6 Score=37.03 Aligned_cols=38 Identities=21% Similarity=0.535 Sum_probs=24.7
Q ss_pred CccCCCCCCCCCceeeeecccC--CCCCCcccccccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYN--LSQPRHFCKNCRRYWTK 69 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn--~~QPRhfCKsCrRYWT~ 69 (330)
...+||.|... .|.-|+.--. ..---..|..|++|+--
T Consensus 225 ~R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 225 VRVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred cCccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 46889999974 4566653221 12223889999999853
No 28
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=49.24 E-value=11 Score=36.43 Aligned_cols=38 Identities=18% Similarity=0.518 Sum_probs=25.3
Q ss_pred CccCCCCCCCCCceeeeecccC----CCCCCcccccccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYN----LSQPRHFCKNCRRYWTK 69 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn----~~QPRhfCKsCrRYWT~ 69 (330)
...+||.|...+ +.-|+.--. ..---..|..|+.|+--
T Consensus 223 ~R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 223 VRVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred cCccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchhh
Confidence 468999999864 555665432 11122689999999843
No 29
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=48.30 E-value=10 Score=27.88 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
..-||+|.+. |..-.. .|+.|..|..
T Consensus 20 ~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 4589999873 554443 6999999974
No 30
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=46.55 E-value=14 Score=28.97 Aligned_cols=31 Identities=23% Similarity=0.556 Sum_probs=25.0
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
+..||+|.+.+|=..|..|. ..-.-|-.|.=
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred CccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 57899999999988888776 55567888853
No 31
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=40.06 E-value=20 Score=34.53 Aligned_cols=31 Identities=19% Similarity=0.530 Sum_probs=22.6
Q ss_pred CCccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 30 HQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 30 ~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
.+..+|++|.+.=.|--. -.+..|||..|++
T Consensus 243 R~GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 243 RAGEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 467899999996555322 2467799999985
No 32
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=37.90 E-value=13 Score=28.60 Aligned_cols=14 Identities=43% Similarity=0.845 Sum_probs=6.0
Q ss_pred CccCCCCCCCCCce
Q 036178 31 QALKCPRCDSLNTK 44 (330)
Q Consensus 31 ~~l~CPRC~S~nTK 44 (330)
-+++|+.|.|.||+
T Consensus 47 lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 47 LGHKCSHCGSYNTR 60 (61)
T ss_dssp T----TTTS---EE
T ss_pred hhhcCCCCCCcccC
Confidence 36899999999997
No 33
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=36.85 E-value=27 Score=30.02 Aligned_cols=39 Identities=21% Similarity=0.590 Sum_probs=33.2
Q ss_pred CCccCCCCCCCCCceeeeecccCCCCCC---ccccccccccc
Q 036178 30 HQALKCPRCDSLNTKFCYYNNYNLSQPR---HFCKNCRRYWT 68 (330)
Q Consensus 30 ~~~l~CPRC~S~nTKFCYYNNYn~~QPR---hfCKsCrRYWT 68 (330)
.-...||+|....--|--++-.+..-|- |.|-.|+--|-
T Consensus 63 ~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 63 QTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 3567899999999988888888887776 89999999884
No 34
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=36.67 E-value=17 Score=36.22 Aligned_cols=36 Identities=28% Similarity=0.694 Sum_probs=22.3
Q ss_pred CCCCCccCCCCCCCCCceeeeecccCC-----CCCCccccccc
Q 036178 27 HQNHQALKCPRCDSLNTKFCYYNNYNL-----SQPRHFCKNCR 64 (330)
Q Consensus 27 ~~~~~~l~CPRC~S~nTKFCYYNNYn~-----~QPRhfCKsCr 64 (330)
..+...-+||||...| ||.---.-. .-..-||+.|.
T Consensus 301 a~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cg 341 (345)
T COG4260 301 AAPAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECG 341 (345)
T ss_pred cCCcccCcchhccccc--cccccCcccccCCccchhhhChhhc
Confidence 3456778999999888 765332111 11346777774
No 35
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=34.71 E-value=35 Score=24.40 Aligned_cols=35 Identities=17% Similarity=0.397 Sum_probs=20.2
Q ss_pred CccCCCCCCCCCceeeeecccCCCC-CCcccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQ-PRHFCKNCRR 65 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~Q-PRhfCKsCrR 65 (330)
+..+||.|.+....+.+........ -.-.|..|.-
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5678999966655555432221111 3345888866
No 36
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.39 E-value=23 Score=25.78 Aligned_cols=32 Identities=31% Similarity=0.571 Sum_probs=25.4
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCCcccccccccccc
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTK 69 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~ 69 (330)
....||.|.....+ .+..-.+.|..|...+.+
T Consensus 27 TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 56779999998877 666777999999876653
No 37
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=32.45 E-value=39 Score=24.31 Aligned_cols=32 Identities=22% Similarity=0.484 Sum_probs=19.1
Q ss_pred cCCCCCCCCCceeeeecccCCCCCCcc-cccccc
Q 036178 33 LKCPRCDSLNTKFCYYNNYNLSQPRHF-CKNCRR 65 (330)
Q Consensus 33 l~CPRC~S~nTKFCYYNNYn~~QPRhf-CKsCrR 65 (330)
.+||.|.+..-.|=+ ...+..-..++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997665532 12333334444 887764
No 38
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=30.90 E-value=23 Score=22.77 Aligned_cols=27 Identities=26% Similarity=0.642 Sum_probs=14.2
Q ss_pred cCCCCCCCCCceeeeecccCCCCCCccccccc
Q 036178 33 LKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCR 64 (330)
Q Consensus 33 l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCr 64 (330)
.+||||...-.++-..+ +.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 57999988776655422 2336777775
No 39
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=30.24 E-value=32 Score=28.80 Aligned_cols=44 Identities=20% Similarity=0.491 Sum_probs=33.0
Q ss_pred CCCccCCCCCCCCCceeeeecccCCCCCCccccccccccccCcccccccCC
Q 036178 29 NHQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVG 79 (330)
Q Consensus 29 ~~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtLRNVPVG 79 (330)
......||-|.....| -..----.|+.|..-|+.|+-....|+|
T Consensus 32 ~~~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 32 QRAKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred HhcCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 3567899999998555 1222337899999999999987776664
No 40
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.05 E-value=36 Score=30.95 Aligned_cols=44 Identities=27% Similarity=0.375 Sum_probs=30.7
Q ss_pred CCCCCCCCCceeeeec---ccCCCCCCccccccccccccCccccccc
Q 036178 34 KCPRCDSLNTKFCYYN---NYNLSQPRHFCKNCRRYWTKGGVLRNVP 77 (330)
Q Consensus 34 ~CPRC~S~nTKFCYYN---NYn~~QPRhfCKsCrRYWT~GGtLRNVP 77 (330)
.||.|.+.+||+-==- .-+.-+-|.-|.+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 6999999999985321 2233456789999998888655544443
No 41
>PRK12496 hypothetical protein; Provisional
Probab=27.48 E-value=36 Score=29.80 Aligned_cols=12 Identities=25% Similarity=0.999 Sum_probs=6.9
Q ss_pred cccccccccccc
Q 036178 58 HFCKNCRRYWTK 69 (330)
Q Consensus 58 hfCKsCrRYWT~ 69 (330)
+.|..|+|++..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 556666666643
No 42
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=27.35 E-value=34 Score=24.45 Aligned_cols=32 Identities=19% Similarity=0.611 Sum_probs=18.2
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
..+||-|.. ..+|..|-+. .-.-..+|..|..
T Consensus 3 h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 468999988 5688866543 2347799999943
No 43
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=26.85 E-value=40 Score=26.83 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=16.9
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCcccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRR 65 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrR 65 (330)
...||-|+..+..|..+.+- -++.|-+|.+
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp EE--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EEECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 46799999887777776543 3799999985
No 44
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=26.85 E-value=47 Score=25.97 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=22.5
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCR 64 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCr 64 (330)
+..||+|..++|=..|..|.- .-.-|-.|.
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred cccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 578999999999988866543 345576664
No 45
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=25.61 E-value=50 Score=28.52 Aligned_cols=31 Identities=26% Similarity=0.657 Sum_probs=24.6
Q ss_pred cCCCCCCCCCceeeeecccCCCCCCccccccccccccCc
Q 036178 33 LKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGG 71 (330)
Q Consensus 33 l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GG 71 (330)
..||.|.|..|- - ...-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 579999997653 2 355699999999998875
No 46
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=25.33 E-value=34 Score=23.28 Aligned_cols=28 Identities=32% Similarity=0.654 Sum_probs=14.6
Q ss_pred cCCCCCCCCCceeeeecccCCCCCCccccccccccc
Q 036178 33 LKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWT 68 (330)
Q Consensus 33 l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT 68 (330)
.+||-|.|..|= ...--+.|..|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 479999998774 5566788999987773
No 47
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.78 E-value=56 Score=32.93 Aligned_cols=34 Identities=32% Similarity=0.709 Sum_probs=23.7
Q ss_pred CCccCCCCCCC-------CCceeeeecccCCCCCCccccccc
Q 036178 30 HQALKCPRCDS-------LNTKFCYYNNYNLSQPRHFCKNCR 64 (330)
Q Consensus 30 ~~~l~CPRC~S-------~nTKFCYYNNYn~~QPRhfCKsCr 64 (330)
+....||+|+. .+.=.|-|=.|...-| ..|..|.
T Consensus 220 g~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~-~~Cp~C~ 260 (505)
T TIGR00595 220 GYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIP-KTCPQCG 260 (505)
T ss_pred cCccCCCCCCCceEEecCCCeEEcCCCcCcCCCC-CCCCCCC
Confidence 45678999994 3445677777776666 4788883
No 48
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=23.36 E-value=31 Score=33.41 Aligned_cols=33 Identities=30% Similarity=0.741 Sum_probs=12.3
Q ss_pred ccCCCCCCCC-CceeeeecccCCCCCCccccccccccc
Q 036178 32 ALKCPRCDSL-NTKFCYYNNYNLSQPRHFCKNCRRYWT 68 (330)
Q Consensus 32 ~l~CPRC~S~-nTKFCYYNNYn~~QPRhfCKsCrRYWT 68 (330)
-..||.|.+. -.+| .-|.+-.-.+|..|..=+-
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 3579999997 5554 3344455699999986553
No 49
>PRK10220 hypothetical protein; Provisional
Probab=23.15 E-value=61 Score=28.13 Aligned_cols=32 Identities=25% Similarity=0.630 Sum_probs=25.0
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCccccccccccccCc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGG 71 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GG 71 (330)
...||.|.|..|- ....-+.|..|.-=|+...
T Consensus 3 lP~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 3 LPHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 3689999997653 2355699999999998774
No 50
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=22.40 E-value=69 Score=27.33 Aligned_cols=29 Identities=28% Similarity=0.440 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCceeeeecccCCCCCCccccccc
Q 036178 32 ALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCR 64 (330)
Q Consensus 32 ~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCr 64 (330)
-+.||-|.+.+|.+--- -.---..|++|.
T Consensus 93 yVlC~~C~spdT~l~k~----~r~~~l~C~aCG 121 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE----GRLIFLKCKACG 121 (125)
T ss_dssp HSSCTSTSSSSEEEEEE----TTCCEEEETTTS
T ss_pred EEEcCCCCCCccEEEEc----CCEEEEEecccC
Confidence 47999999999997654 112335688885
No 51
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.13 E-value=1e+02 Score=25.66 Aligned_cols=36 Identities=22% Similarity=0.443 Sum_probs=25.3
Q ss_pred CCCccCCCCCCCCCceeeeecccCCCCCCccccccccccc
Q 036178 29 NHQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWT 68 (330)
Q Consensus 29 ~~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT 68 (330)
......||.|.+ .+--|=+.. ..+.+.|..|.-|-.
T Consensus 18 lpt~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 18 LPKIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred CCcEeECCCCCC-eEeeeecCC---CcceEECCCCCCccC
Confidence 356789999995 233333433 478899999999854
No 52
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.44 E-value=63 Score=22.18 Aligned_cols=32 Identities=19% Similarity=0.484 Sum_probs=18.2
Q ss_pred CCCCCCCCCceeeeecccCCCCCCccccccccccccC
Q 036178 34 KCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKG 70 (330)
Q Consensus 34 ~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~G 70 (330)
-||.|... .|..... ...|+.|..|...+-..
T Consensus 2 FCp~Cg~~----l~~~~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNM----LIPKEGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCc----cccccCC-CCCEEECCcCCCeEECC
Confidence 48888762 2333221 12478888888665444
No 53
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=20.77 E-value=63 Score=26.87 Aligned_cols=44 Identities=23% Similarity=0.420 Sum_probs=30.8
Q ss_pred CCCccCCCCCCCCCceeeeecccCCCCCCccccccccccccCcccccccCC
Q 036178 29 NHQALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVG 79 (330)
Q Consensus 29 ~~~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtLRNVPVG 79 (330)
......||.|....-|= ..-----|+.|.+-|+.|.-..+-|.|
T Consensus 33 q~a~y~CpfCgk~~vkR-------~a~GIW~C~~C~~~~AGGAy~~~T~~~ 76 (90)
T PTZ00255 33 QHAKYFCPFCGKHAVKR-------QAVGIWRCKGCKKTVAGGAWTLSTPAA 76 (90)
T ss_pred HhCCccCCCCCCCceee-------eeeEEEEcCCCCCEEeCCccccccchh
Confidence 35679999998766550 001227899999999988876665554
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=20.68 E-value=37 Score=26.99 Aligned_cols=11 Identities=45% Similarity=1.226 Sum_probs=9.3
Q ss_pred CCccCCCCCCC
Q 036178 30 HQALKCPRCDS 40 (330)
Q Consensus 30 ~~~l~CPRC~S 40 (330)
+.-+.||||+-
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 56799999985
No 55
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=20.36 E-value=31 Score=34.87 Aligned_cols=38 Identities=26% Similarity=0.584 Sum_probs=29.6
Q ss_pred CccCCCCCCCCCceeeeecccCCCCCCccccccccccccCcccccccCCCCcC
Q 036178 31 QALKCPRCDSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCR 83 (330)
Q Consensus 31 ~~l~CPRC~S~nTKFCYYNNYn~~QPRhfCKsCrRYWT~GGtLRNVPVGGG~R 83 (330)
-.++|-.|-+.-. --+|+||..|. ++||+.+.|--+.+
T Consensus 241 ~iLRCh~Cfsit~----------~m~k~FCp~CG-----~~TL~K~aVsv~~d 278 (376)
T KOG2463|consen 241 YILRCHGCFSITS----------EMPKDFCPSCG-----HKTLTKCAVSVDED 278 (376)
T ss_pred heeEeeeeeEecC----------ccchhcccccC-----CCeeeEEEEEecCC
Confidence 5689999987653 37899999996 56999888766655
Done!